TIGR Closure Tools

Project Overview

This is software for the whole-genome shotgun method of sequencing DNA: randomly selected fragments of sheared DNA are cloned in libraries characterized by fragment size; both ends of each fragment are sequenced by Sanger chemistry with an instrument such as the ABI 3730; fragment reads are computationally re-assembled with software such as the Celera Assembler; gaps in the assembly are closed by manual inspection, directed re-sequencing, and regional re-assembly; finished sequence is fed to software or teams of experts for annotation that reveals the encoded gene content. This software was developed at TIGR where it contributed to the sequencing and publication of hundreds of microbial genomes.

This package of tools includes...

1. AutoCloser and components such as makeReactions and casper
2. Clover and components such as Oats
3. autoPrimer wrapper for p3
4. getqc analysis for closure databases
5. SQL scripts for closure databases
6. importTraces for loading closure databases with data from the NCBI Trace Archive
7. subfrag for manipulation of Celera Assembler input files
8. pullfrag for generation of Celera Assembler input from closure databases
9. aloader for upload of Celera Assembler output into closure databases

Developer Resources

• Start with the PROJECT PAGE on Source Forge.
• The code in this package is under SVN VERSION CONTROL. (The CVS and package downloads are out of date.)
• The SourceForge DATABASE of bug reports and feature requests.

This software was developed at The Institute for Genomic Research (TIGR) with financial assistance from the Microbial Sequencing Centers (MSC), part of the National Institute of Allergy and Infectious Disease (NIAID) at the National Insitutes of Health (NIH). The source is hosted by SourceForge.